Week Name Description
File Syllabus
File Calendar
URL Bioinformatics Programming Using Python
URL Final Project Groups
23 January - 29 January File M01 Notes: Descriptive statistics
File M01 Presentation: Introduction
File M01 Handout 01: Probability
File Reading: Qin Nature 2010
File Problems 00: Pre-test
File Problems 01: Quantitative methods
File W01 Notes: Inference and machine learning
30 January - 5 February File M02 Notes: Introduction to Python
File M02 Notes: Python primitives
File M02 Handout 02: Installing Python
File M02 Handout 03: Submitting Python problems
Page Reading: Bioinformatics Programming
File Reading: Dudley PLoS CB 2009
File Problems 02: Introduction to Python
File W02 Notes: References
File W02 Notes: Functions
6 February - 12 February File W03 Notes: Modules and I/O
File W03 Handout 04: I/O
Page Reading: Bioinformatics Programming
File Reading: Cock Bioinformatics 2009
File Problems 03: I/O and Regular Expressions
13 February - 19 February File M04 Notes: Regular Expressions
Page Reading: Regular Expressions
File W04 Notes: Network resources and data stores
Page Reading: Bioinformatics Programming
File Reading: Noble PLoS CB 2009
File Problems 04: Regular Expressions, Downloads, and Data Stores
20 February - 26 February Page Reading: Command line tools
File W05 Notes: Computational project management and tools
27 February - 5 March File M06: Genomes and sequence alignment
File M06 Presentation: Genomic data resources
Page Reading: Bioinformatics and Functional Genomics
File Reading: Sela PNAS 2008
File W06 Notes: High-throughput sequencing
File W06 Presentation: High-throughput sequencing
File W06 Presentation: 454 sequencing
File W06 Presentation: Illumina sequencing
Page Reading: Bioinformatics and Functional Genomics
File Problems 05: Genomes and Sequencing
File Problems 05: Genomes and Sequencing (data)
Folder B.longum from GenBank FTP
Use these files for Problem 4 if you can't connect to GenBank FTP yourself.
6 March - 12 March File M07 Presentation: Metagenomics
Page Reading: Bioinformatics and Functional Genomics
File Reading: Venter Science 2004
URL W07: Comparative Genomics
File Problems 06: Meta- and Comparative Genomics
File Problems 06: Meta- and Comparative Genomics (data)
13 March - 19 March File M08: Microarray Data
Page Reading: Microarrays
File Reading: Hughes 2000 Cell
File W08: Microarray Analysis
File Problems 07: Microarrays
File Problems 07: Microarrays (data)
File gcrma.pcl
27 March - 2 April File M09 Presentation: Epigenetics
Page Reading: Epigenetics and Regulation
File Reading: Workman Science 2005
File W09 Presentation: Transcriptional Regulation
File Problems 08: Regulation
3 April - 9 April File M10 Presentation: Proteins
Page Reading: Proteins and PPIs
File Reading: Mohan PLoS CB 2009
File W10 Presentation: PPIs
File Problems 09: Review
10 April - 16 April File M11 Presentation: Genetic Interactions
Page Reading: Genetic and Disease Interactions
File Reading: Costanzo Science 2010
File W11 Presentation: Network Integration
File Problems 10: Network Integration